Genome organization in prokaryotes

Most of the well-characterized prokaryotic genomes consist of double-stranded DNA organized as a single circular chromosome 0.6–10 Mb in length and one or more circular plasmid species of 2 kb-1.7 Mb. The past few years, however, have revealed some major variations in genome organization. In addition, a recent accumulation of data has shown that the location and orientation of the genes and repeated sequences (including prophages and transposons) on and among these elements is not always random. Some of the non-randomness is probably the result of unique historical events; in other cases it reflects selection for the optimization of function.     

Genome organization and species formation in vertebrates

Some years ago Wilson and co-workers proposed that the higher rates of karyotypic change and species formation of mammals compared to cold-blooded vertebrates are due to the formation of small demes, as favored by the social structuring and brain development of the former. Here, evidence is reviewed which indicates that mammals are more prone to karyotypic change and species formation than cold-blooded vertebrates because of their different genome organization. Similar evidence has also recently become available for birds. While this different organization appears to be a necessary and, in all likelihood, a sufficient condition for the increased rates of karyotypic change and species formation found in mammals, it is still possible that social structuring and brain development may have played an additional accelerating role.This paper was presented at the International Conference on Genome Plasticity held in Cancun, Mexico (December 8–12, 1991)     

Studies on chromatin organization in a nucleolus without fibrillar centres

In embryonic cell-line derivative KCo of Drosophila melanogaster, the nucleolus, like most nucleoli, contains a small proportion of ribosomal DNA (1-2% of the total nucleolar DNA). The ribosomal DNA is virtually the only active gene set in the nucleolus and is found among long stretches of inactive supercoiled heterochromatic segments. We have demonstrated by use of a Feulgen-like ammine-osmium staining procedure that, depending on the state of growth, more or less fibres of decondensed DNA emanating from the intra-nucleolar chromatin (which is in continuity with the nucleolus-associated chromatin) ramify and unravel within the central nucleolar core to be transcribed. The nucleolus expands or contracts with the variation of activity and could belong to a supramolecular matricial structure such as is shown after extraction of the nuclei. After a long period of exposure to high doses of actinomycin D, the central nucleolar core became an homogeneous fibrous structure that could be interpreted as an aggregate of protein skeletal elements. The mechanism of repression and derepression of the nucleolar chromatin could thus be explained by a mechanism involving in part a sub-nucleolar structure. We propose a schematic organization of the nucleolar chromatin in KCo cells of Drosophila and discuss it in relation with other nucleolar organizations.     

Genome DNA content and chromosome organization in Gossypium

The ascending genome size in Gossypium is assumed to be D, A, B, E and F, and C. Feulgen cytophotometry revealed that mean value of DNA content for each genome was D= 10.95, B = 13.88, F = 14.31, E = 18.24, A = 18.66, and C = 20.30, and that there is a close relationship of genomic chromosome size and DNA content. Evidence suggests that the five genomes with large chromosomes arose from a D genome-like progenetor by large scale, saltatory replication of repetitive DNA distributed uniformly through the ancestral genome. Corresponding adjustment in recombination units did not accompany the two-fold divergence in DNA value of the two homoeologous A and D genomes in the allotetraploid species.     

The nucleolus: a model for the organization of nuclear functions

Nucleoli are the prominent contrasted structures of the cell nucleus. In the nucleolus, ribosomal RNAs (rRNAs) are synthesized, processed and assembled with ribosomal proteins. The size and organization of the nucleolus are directly related to ribosome production. The organization of the nucleolus reveals the functional compartmentation of the nucleolar machineries that depends on nucleolar activity. When this activity is blocked, disrupted or impossible, the nucleolar proteins have the capacity to interact independently of the processing activity. In addition, nucleoli are dynamic structures in which nucleolar proteins rapidly associate and dissociate with nucleolar components in continuous exchanges with the nucleoplasm. At the time of nucleolar assembly, the processing machineries are recruited in a regulated manner in time and space, controlled by different kinases and form intermediate structures, the prenucleolar bodies. The participation of stable pre-rRNAs in nucleolar assembly was demonstrated after mitosis and during development but this is an intriguing observation since the role of these pre-rRNAs is presently unknown. A brief report on the nucleolus and diseases is proposed as well as of nucleolar functions different from ribosome biogenesis.Robert Feulgen Lecture presented at the 48th Symposium of the Society for Histochemistry in Stresa, Lake Maggiore, Italy, 7–10 September 2006.     

Genome organization and polymorphism of the murine beta-glucuronidase region

Thirty-eight kilobases of mouse genomic DNA which surround and include the coding sequences for beta-glucuronidase has been mapped. Intron-exon arrangements were determined by hybridization of genomic sequences with cDNA clones, and minimum estimates of gene length (11-17 kb) and intron number were obtained. Only a single gene was observed when genomic DNA was probed with subclones containing beta-glucuronidase coding sequence; there was no evidence of duplicated or pseudogenes. However, sequences distal to the 3' end of the gene are present elsewhere in the genome in a limited number of copies. Eight haplotypes of the beta-glucuronidase region with differing regulatory genotypes were compared for restriction fragment polymorphisms. Surprisingly little was found, considering the diverse origin of the haplotypes. Two of the polymorphisms that were found may be correlated with regulatory phenotypes. A BamHI site is missing from the CS and CL haplotypes that share regulatory properties, and a 0.2-kb insertion is consistently present in haplotypes showing increased response to induction by androgens in kidney.     

Genome organization: balancing stability and plasticity

The cell needs to stably maintain its genome and protect it from uncontrolled modifications that would compromise its function. At the same time, the genome has to be a plastic structure that can dynamically (re)organize to allow the cell to adopt different functional states. These dynamics occur on the nanometer to micrometer length scale, i.e. ranging from the level of single proteins up to that of whole chromosomes, and on a microsecond to hour time scale. Here, we review different contributions to the dynamic features of the genome, describe how they are determined experimentally, and discuss the results of these measurements in terms of how the requirements for stability and plasticity are accommodated with specific activities in the nucleus.     

Genome organization and expression of the rat ACBP gene family

Acyl-CoA-Binding Protein (ACBP)/Diazepam-Binding Inhibitor (DBI) is a 10 kD protein which has been implicated in a surprisingly large number of biochemical functions. We have unambiguously demonstrated that ACBP binds acyl-CoA esters with high affinity andin vivo functions as an acyl-CoA ester pool former. We have molecularly cloned and characterized the rat ACBP gene family which comprises one expressed and four processed pseudogenes. One of these was shown to exist in two allelic forms. A comprehensive computer-aided analysis of the promoter region of the expressed ACBP gene revealed that it exhibits all the hallmarks of typical housekeeping genes. In addition, the promoter region harbors a number of ptential tissue specific cis-acting elements that may in part regulate the level of ACBP expression in specialized cells.     

Genome organization and characterization of mycobacteriophage Bxb1

Mycobacteriophage Bxb1 is a temperate phage of Mycobacterium smegmatis. The morphology of Bxb1 particles is similar to that of mycobacteriophages L5 and D29, although Bxb1 differs from these phages in other respects. First, it is heteroimmune with L5 and efficiently forms plaques on an L5 lysogen. Secondly, it has a different host range and fails to infect slow-growing mycobacteria, using a receptor system that is apparently different from that of L5 and D29. Thirdly, it is the first mycobacteriophage to be described that forms a large prominent halo around plaques on a lawn of M. smegmatis. The sequence of the Bxb1 genome shows that it possesses a similar overall organization to the genomes of L5 and D29 and shares weak but detectable DNA sequence similarity to these phages within the structural genes. However, Bxb1 uses a different system of integration and excision, a repressor with different specificity to that of L5 and encodes a large number of novel gene products including several with enzymatic functions that could degrade or modify the mycobacterial cell wall.